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- EMDB-61108: Cryo-EM structure of human Alpha-7 nicotinic acetylcholine receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-61108
TitleCryo-EM structure of human Alpha-7 nicotinic acetylcholine receptor
Map data
Sample
  • Complex: AChR7 nicotinic acetylcholine receptor
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
KeywordsReceptors / Inhibitor / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory processing / synaptic transmission involved in micturition / response to acetylcholine / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / chloride channel regulator activity / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity ...sensory processing / synaptic transmission involved in micturition / response to acetylcholine / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / chloride channel regulator activity / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / acetylcholine binding / dendritic spine organization / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / response to amyloid-beta / positive regulation of protein metabolic process / negative regulation of tumor necrosis factor production / modulation of excitatory postsynaptic potential / plasma membrane raft / monoatomic ion channel activity / toxic substance binding / monoatomic ion transport / negative regulation of cytokine production involved in inflammatory response / positive regulation of excitatory postsynaptic potential / positive regulation of long-term synaptic potentiation / response to nicotine / negative regulation of canonical NF-kappaB signal transduction / regulation of membrane potential / excitatory postsynaptic potential / synapse organization / cognition / calcium channel activity / memory / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / monoatomic ion transmembrane transport / chemical synaptic transmission / learning or memory / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / postsynaptic membrane / neuron projection / postsynapse / positive regulation of cell population proliferation / synapse / dendrite / endoplasmic reticulum membrane / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu R / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122064 China
CitationJournal: To Be Published
Title: Cryo-EM structure of human Alpha-7 nicotinic acetylcholine receptor
Authors: Lei RY / Hui JZ
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61108.png

Downloads & links

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Map

FileDownload / File: emd_61108.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.853
Minimum - Maximum-6.513542 - 8.699759500000001
Average (Standard dev.)-0.00039863068 (±0.22375722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 307.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61108_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61108_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AChR7 nicotinic acetylcholine receptor

EntireName: AChR7 nicotinic acetylcholine receptor
Components
  • Complex: AChR7 nicotinic acetylcholine receptor
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL

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Supramolecule #1: AChR7 nicotinic acetylcholine receptor

SupramoleculeName: AChR7 nicotinic acetylcholine receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuronal acetylcholine receptor subunit alpha-7

MacromoleculeName: Neuronal acetylcholine receptor subunit alpha-7 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.211445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GEFQRKLYKE LVKNYNPLER PVANDSQPLT VYFSLSLLQI MDVDEKNQVL TTNIWLQMSW TDHYLQWNVS EYPGVKTVRF PDGQIWKPD ILLYNSADER FDATFHTNVL VNSSGHCQYL PPGIFKSSCY IDVRWFPFDV QHCKLKFGSW SYGGWSLDLQ M QEADISGY ...String:
GEFQRKLYKE LVKNYNPLER PVANDSQPLT VYFSLSLLQI MDVDEKNQVL TTNIWLQMSW TDHYLQWNVS EYPGVKTVRF PDGQIWKPD ILLYNSADER FDATFHTNVL VNSSGHCQYL PPGIFKSSCY IDVRWFPFDV QHCKLKFGSW SYGGWSLDLQ M QEADISGY IPNGEWDLVG IPGKRSERFY ECCKEPYPDV TFTVTMRRRT LYYGLNLLIP CVLISALALL VFLLPADSGE KI SLGITVL LSLTVFMLLV AEIMPATSDS VPLIAQYFAS TMIIVGLSVV VTVIVLQYHH HDPDGGKMPK WTRVILLNWC AWF LRMKRP GEDKVRPACQ HKQRRCSLAS VEMSAVAPPP ASNGNLLYIG FRGLDGVHCV PTPDSGVVCG RMACSPTHDE HLLH GGQPP EGDPDLAKIL EEVRYIANRF RCQDESEAVC SEWKFAACVV DRLCLMAFSV FTIICTIGIL MSAPNFVEAV SKDFA

UniProtKB: Neuronal acetylcholine receptor subunit alpha-7

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 5 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7koo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59900
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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